Difference between revisions of "Publications"
From Chuang Lab
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[https://www.biorxiv.org/content/10.1101/790246v1 Yvonne A. Evrard, Anuj Srivastava, Jelena Randjelovic, Sasi Arunachalam, Carol J. Bult, Huiqin Chen, Lily Chen, Michael Davies, Sherri Davies, Brandi Davis-Dusenbery, Jack DiGiovanna, Li Ding, James H. Doroshow, Bingliang Fang, Christian Frech, Ramaswamy Govindan, Min Jin Ha, Meenhard Herlyn, Ryan Jeon, Andrew Kossenkov, Michael T. Lewis, Shunqiang Li, Michael Lloyd, Funda Meric-Bernstam, Nevena Miletic, Jeffrey A. Moscow, Steven Neuhauser, David Nix, Rajesh Patidar, Vito Rebecca, Peter N. Robinson, Jacqueline Rosains, Jack Roth, Isheeta Seth, Tamara Stankovic, Adam Stanojevic, Brian A. Van Tine, Alana L. Welm, Bryan E. Welm, Jayamanna Wickramasinghe, XingYi Woo, Min Xiao, Zi-ming Zhao, Dennis A. Dean II, Jeffrey S. Morris, Jeffrey H. Chuang. Biorxiv preprint.] | [https://www.biorxiv.org/content/10.1101/790246v1 Yvonne A. Evrard, Anuj Srivastava, Jelena Randjelovic, Sasi Arunachalam, Carol J. Bult, Huiqin Chen, Lily Chen, Michael Davies, Sherri Davies, Brandi Davis-Dusenbery, Jack DiGiovanna, Li Ding, James H. Doroshow, Bingliang Fang, Christian Frech, Ramaswamy Govindan, Min Jin Ha, Meenhard Herlyn, Ryan Jeon, Andrew Kossenkov, Michael T. Lewis, Shunqiang Li, Michael Lloyd, Funda Meric-Bernstam, Nevena Miletic, Jeffrey A. Moscow, Steven Neuhauser, David Nix, Rajesh Patidar, Vito Rebecca, Peter N. Robinson, Jacqueline Rosains, Jack Roth, Isheeta Seth, Tamara Stankovic, Adam Stanojevic, Brian A. Van Tine, Alana L. Welm, Bryan E. Welm, Jayamanna Wickramasinghe, XingYi Woo, Min Xiao, Zi-ming Zhao, Dennis A. Dean II, Jeffrey S. Morris, Jeffrey H. Chuang. Biorxiv preprint.] | ||
| − | ''' | + | '''Deep learning-based cross-classifications reveal conserved spatial behaviors within tumor histological images''' <div> |
| − | [https://doi.org/10.1101/715656 Javad Noorbakhsh, Saman Farahmand, Mohammad Soltanieh-ha | + | [https://doi.org/10.1101/715656 Javad Noorbakhsh , Saman Farahmand, Ali Foroughi pour, Sandeep Namburi, Dennis Caruana, David Rimm, Mohammad Soltanieh-ha, Kourosh Zarringhalam, and Jeffrey H Chuang. Biorxiv preprint] |
'''pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks''' <div> | '''pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks''' <div> | ||
Revision as of 14:49, 3 March 2020
In reverse chronological order.
Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts
Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and Analysis
Deep learning-based cross-classifications reveal conserved spatial behaviors within tumor histological images
pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks
Henry B. Zhang, Minji Kim, Jeffrey H. Chuang, Yijun Ruan. Bioinformatics (2020), in press
MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms
Longitudinal molecular trajectories of diffuse glioma patients.
Barthel FP, Johnson KC, Varn FS, Moskalik AD, Tanner G, Kocakavuk E, Anderson KJ, Abiola O, Aldape K, Alfaro KD, Alpar D, Amin SB, Ashley DM, Bandopadhayay P, Barnholtz-Sloan JS, Beroukhim R, Bock C, Brastianos PK, Brat DJ, Brodbelt AR, Bruns AF, Bulsara KR, Chakrabarty A, Chakravarti A, Chuang JH, Claus EB, Cochran EJ, Connelly J, Costello JF, Finocchiaro G, Fletcher MN, French PJ, Gan HG, Gilbert MR, Gould PV, Grimmer MR, Iavarone A, Ismail A, Jenkinson MD, Khasraw M, Kim H, Kouwenhoven MCW, LaViolette PS, Li M, Lichter P, Ligon KL, Lowman AK, Malta TM, Mazor T, McDonald KL, Molinaro AM, Nam DH, Nayyar N, Ng HK, Ngan CY, Niclou SP, Niers JN, Noushmehr H, Noorbakhsh J, Ormond DR, Park CK, Poisson LM, Rabadan R, Radlwimmer B, Rao G, Reifenberger G, Sa JS, Schuster M, Shaw BL, Short SC, Sillevis Smitt PA, Sloan AE, Smits M, Suzuki H, Tabatabai G, Van Meir EG, Watts C, Weller M, Wesseling P, Westerman BA, Widhalm G, Woehrer A, Yung WKA, Zadeh G, Huse JT, de Groot JF, Stead LF, Verhaak RGW, the GLASS Consortium. Nature, Nature 576:112–120 (2019) doi: 10.1038/s41586-019-1775-1.
Molecular biology and evolution of cancer: from discovery to action
Treating cancer as an invasive species
BMP signaling mediates glioma stem cell quiescence and confers treatment resistance in glioblastoma
Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines
The implications of frameshift mutation burden on immune cell landscape and survival outcome in patients with non-small cell lung cancer (NSCLC)
Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors
Unstable Genome and Transcriptome Dynamics during Tumor Metastasis Contribute to Therapeutic Heterogeneity in Colorectal Cancers.
Mutations in DNA repair genes are associated with increased neoantigen burden and a distinct immunophenotype in lung squamous cell carcinoma
CCNE1 Amplification Is Associated with Poor Prognosis in Patients with Triple Negative Breast Cancer
Whole-exome sequencing capture kit biases yield false negative mutation calls in TCGA cohorts
Victor G. Wang, Hyunsoo Kim, Jeffrey H. Chuang. PLoS ONE 13(10): e0204912. (2018).
High-resolution deconstruction of evolution induced by chemotherapy treatments in breast cancer xenografts
Hyunsoo Kim, Pooja Kumar, Francesca Menghi, Javad Noorbakhsh, Eliza Cerveira, Mallory Ryan, Qihui Zhu, Guruprasad Ananda, Joshy George, Henry Chen, Susan Mockus, Chengsheng Zhang, Yan Yang, James Keck, R. Krishna Murthy Karuturi, Carol J Bult, Charles Lee, Edison T Liu, Jeffrey H Chuang. Scientific Reports 8: 17937 (2018).
Distribution-based measures of tumor heterogeneity are sensitive to mutation calling and lack strong clinical predictive power
Javad Noorbakhsh, Hyunsoo Kim, Sandeep Namburi, Jeffrey Chuang. Scientific Reports 8:11445 DOI:10.1038/s41598-018-29154-7 (2018).
SARNAclust: Semi-Automatic Detection Of RNA Protein Binding Motifs From Immunoprecipitation Data
Alterations in the Rho pathway contribute to Epstein-Barr virus-induced lymphomagenesis in immunosuppressed environments
Mutations in DNA repair genes are associated with increased neo-antigen load and activated T cell infiltration in lung adenocarcinoma
Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures
Javad Noorbakhsh and Jeffrey H Chuang, Nature Genetics 49, 1288–1289 doi:10.1038/ng.3876 (2017).
CloudNeo: A cloud pipeline for identifying patient-specific tumor neoantigens
Activation of GCN2 by Ribosome Stalling Links Translation Elongation with Translation Initiation
The Tandem Duplicator Phenotype as a Distinct Genomic Configuration in Cancer
Genetic Architectures of Quantitative Variation in RNA Editing Pathways
Loss of Tumor Suppressive MicroRNA-31 Enhances TRADD/NF-κB Signaling in Glioblastoma
Identification of Tumor Subtypes of Endometrial Carcinoma by Integration of Heterogeneous Datasets
Hyunsoo Kim, Markus Bredel, Haesun Park, Jeffrey H Chuang. J Med Diagn Meth 4:189 (2015).
Functional chromatin features are associated with structural mutations in cancer
Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration
Ryuta Ishimura, Gabor Nagy, Ivan Dotu, Huihao Zhou, Xiang-Lei Yang, Paul Schimmel, Satoru Senju, Yasuharu Nishimura, Jeffrey H. Chuang, and Susan L. Ackerman. Science 345, 455–459 (2014).
Dynamics of the ethanolamine glycerophospholipid remodeling network
Integrating chemical footprinting data into RNA secondary structure prediction
Statistical analysis of the processes controlling choline and ethanolamine glycerophospholipid molecular species composition
Transcriptional Enhancers in Protein-Coding Exons of Vertebrate Developmental Genes
Deborah I Ritter, Zhiqiang dong, Su Guo, Jeffrey H Chuang, PLoS ONE 7(5): e35202 (2012). doi:10.1371/journal.pone.0035202.
CodingMotif: Exact Determination of Overrepresented Nucleotide Motifs in Coding Sequences
Yang Ding, William A Lorenz and Jeffrey H Chuang. BMC Bioinformatics. 13:32 (2012).
Expression divergence measured by transcriptome sequencing of four yeast species
A Mathematical Model for the Determination of Steady-State Cardiolipin Remodeling Mechanisms Using Lipidomic Data
A molecular-imprint nanosensor for ultrasensitive detection of proteins
Dong Cai, Lu Ren, Huaizhou Zhao, Chenjia Xu, Lu Zhang, Ying Yu, Hengzhi Wang, Yucheng Lan, Mary F. Roberts, Jeffrey H. Chuang, Michael J. Naughton, Zhifeng Ren and Thomas C. Chiles. Nature Nanotechnology 5:597 (2010).
- Highlight on Nature Chemistry
- Highlight on Nature Methods
The Importance of Being Cis: Evolution of Orthologous Fish and Mammalian Enhancer ActivityDynamic simulation of cardiolipin remodeling: Greasing the wheels for an interpretative approach to lipidomicsMichael A. Kiebish, Rob Bell, Kui Yang, Toan Phan, Zhongdan Zhao, William Ames, Thomas N. Seyfried, Richard W. Gross, Jeffrey H. Chuang, and Xianlin Han. J. Lipid Res. 51:2153 (2010).A systematic approach to identify functional motifs within vertebrate developmental enhancersQiang Li, Deborah Ritter, Nan Yang, Zhiqiang Dong, Hao Li, Jeffrey H. Chuang, Su Guo. Developmental Biology 337:484 (2010).COMIT: Identification of Noncoding Motifs under Selection in Coding SequencesDeniz Kural, Yang Ding, Jiantao Wu, Alicia M Korpi, and Jeffrey H. Chuang. Genome Biology 10:R133 (2009).The effect of Plasmodium falciparum Sir2a histone deacetylase on clonal and longitudinal variation in expression of the var family of virulence genesWeak preservation of local neutral mutation rates across mammalian genomesHideo Imamura, John E Karro and Jeffrey H. Chuang. BMC Evolutionary Biology (2009), 9:89
Cardiolipin and electron transport chain abnormalities in mouse brain tumor mitochondria: Lipidomic evidence supporting the Warburg theory of cancercneViewer: A Database of Conserved Noncoding Elements for Studies of Tissue-Specific Gene RegulationJ. Persampieri, D. I. Ritter, D. Lees, J. Lehoczky, Q. Li, S. Guo, and Jeffrey H. Chuang. Bioinformatics, 24:2418-2419 (2008).- cneViewer website Brain Mitochondrial Lipid Abnormalities in Mice Susceptible to Spontaneous Gliomas.
M.A. Kiebish, X. Han, H. Cheng, Jeffrey H. Chuang, and T.N. Seyfried. Lipids 43, 951-9 (2008).
Measuring the Prevalence of Regional Mutation Rates: An Analysis of Silent Substitutions in Mammals, Fungi, and Insects.A.K. Fox, B.B. Tuch, and Jeffrey H. Chuang. BMC: Evolutionary Biology, 8, 186 (2008).
Lipidomic Analysis and Electron Transport Chain Activities in C57BL/6J Mouse Brain Mitochondria.Similarity of Synonymous Substitutions Rates Across Mammalian Genomes.Jeffrey H. Chuang and H. Li. Journal of Molecular Evolution, 65, 236 (2007).Sequences Conserved by Selection across Mouse and Human Malaria Species.H. Imamura, J. Persampieri, and Jeffrey H. Chuang. BMC: Genomics, 8, 372 (2007).- PDF
- Supplementary Materials Website
Smart Polymers: Applications in Biotechnology and Biomedicine, Second Edition. Chapter title: Imprinting Using Smart Polymers.C. Alvarez-Lorenzo, A. Concheiro, Jeffrey Chuang and A. Yu. Grosberg. CRC Press: Boca Raton (2007).Genome-wide Regulatory Complexity in Yeast Promoters: Separation of Functional and Neutral Sequence.C.S. Chin, Jeffrey H. Chuang, and H. Li. Genome Research, 15, 205 (2005).- PDF
- Supplementary Materials Website
Functional Bias and Spatial Organization of Genes in Mutational Hot and Cold Regions in the Human Genome.Jeffrey Chuang and H. Li, PLOS Biology, 2, 0253, doi:10.1371/journal.pbio (2004).- PDF
- Synopsis
Multiple Contact Adsorption of Target Molecules by Heteropolymer Gels.K. Ito, J. Chuang, C. Alvarez-Lorenzo, T. Watanabe, N. Ando, and A. Yu. Grosberg, Macromolecular Symposia 207, 1 (2004).Multiple point adsorption in a Heteropolymer Gel and the Tanaka Approach To Imprinting: Experiment and Theory.K. Ito, Jeffrey Chuang, C. Alvarez-Lorenzo, T. Watanabe, N. Ando, and A. Yu. Grosberg, Progress in Polymer Science, 28, 1489 (2003).Anomalous Dynamics of Translocation.Jeffrey Chuang, Y. Kantor, and M. Kardar, Physical Review E, 65, 011802 (2001).Effect of Reversible Cross-linker, N,N'-Bis(acryloyl)-cystamine, on Calcium Ion Adsorption by Imprinted Gels.H. Hiratani, C. Alvarez-Lorenzo, Jeffrey Chuang, O. Guney, A. Yu.Grosberg, and T. Tanaka, Langmuir, 17, 4431 (2001).Free Energy Self-Averaging in Protein-Sized Heteropolymers.Jeffrey Chuang, A. Yu. Grosberg, and M. Kardar, Physical Review Letters, 87, 078104 (2001).Frustrations in Polymer Gels and Their Minimization through Molecular Imprinting.
- Supplementary Materials Website
- PDF
